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treangenlab / komb

KOMB is a tool for fast identification of unitigs of interest in metagenomes. KOMB introduces the concept of a Hybrid Unitig Graph (an extension to compacted de Bruijn graphs) and relies on k-core and K-truss decomposition algorithms.
GNU General Public License v2.0
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Fix to support newer version of the igraph library #1

Closed nsapoval closed 1 year ago

nsapoval commented 1 year ago

@kanaifu has implemented a fix, so that KOMB can support newer versions of the igraph library. The change is not reverse-compatible, so going forward we will only be supporting the new igraph API.

kanaifu commented 1 year ago

Verified. igraph>=0.10.4 required now.

szhorvat commented 1 year ago

igraph>=0.10.4 required now.

Given the updates you made, everything should work with any 0.10.x version, including 0.10.0. There should be no need to pin the version to 0.10.4 specifically, as in the README, unless you used functions which are clearly marked as experimental in the documentation. But this is not the case here. If you see any unexpected breakage, please open an issue in the igraph repo.

nsapoval commented 1 year ago

Thanks for catching that, I'll modify README and conda environment YAML to igraph>=0.10.0.

szhorvat commented 1 year ago

Regarding the concern about breaking changes that's mentioned in the README:

There will be several breaking changes in version 0.11, but they might not affect this project. 0.10 had the most severe disruption due to the move to integers indices in general, and 64-bit integers specifically. We are working towards a 1.0 release (probably the next one after 0.11), after which the intention is to keep the API stable in the longer term.